User: dineli_karunathilaka

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Posts by dineli_karunathilaka

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Comment: C: Trimmomatic in Galaxy
... Hi Jen, Is there any update on this?? ...
written 15 months ago by dineli_karunathilaka10
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Comment: C: Trimmomatic in Galaxy
... Hi Jen, I have my own galaxy instance. But I tried replicating the issue on 'usegalaxy' as well. Problem is it never display an error on the history instead it publishes an error message on the galaxy dashboard. (refer the image) Thus I am unable to report it as a bug. Since I got the internal serv ...
written 15 months ago by dineli_karunathilaka10
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Comment: C: Trimmomatic workflow error - failed to find output_name
... Hi Jen, I'm working on my own Galaxy instance setup on my server. I have tested according what you have suggested several times but the problem still exists. I executed the same workflow on the 16.10 version, still the same issue. Dineli ...
written 15 months ago by dineli_karunathilaka10
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Comment: C: Trimmomatic in Galaxy
... Thanks Peter for the explanation. I did as you and Jen suggested but i'm getting the below error. Exception: Workflow evaluation problem - failed to find output_name fastq_out_r1_paired in step_outputs {u'fastq_out_paired': , u'fastq_out_unpaired': } galaxy.workflow.run ERROR 2016-09-28 17:42:06,4 ...
written 15 months ago by dineli_karunathilaka10
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Comment: C: Trimmomatic in Galaxy
... Thank you very much for your feedback Jen. I am a newbie to Galaxy thus I have several questions. Are you are suggesting to use 2 trimmomatc tools?(1 for crop and other for clip) If so how can I connect the 2 tools? I mean, output from the first trimmomatic should use as the input for the 2nd tool ...
written 15 months ago by dineli_karunathilaka10
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Trimmomatic workflow error - failed to find output_name
... Hi, I am getting a error while executing a workflow which involves trimmomatic and bwa tools. Initially a paired data set is sent as an input to the trimmomatic and the outputs fastq_out_r1_paired and fastq_out_r2_paired are sent as inputs to the BWA. Error is as below : Exception: Workflow evalu ...
trimmomatic exception galaxy workflow written 15 months ago by dineli_karunathilaka10 • updated 15 months ago by Jennifer Hillman Jackson23k
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Trimmomatic in Galaxy
... Hi, Is there a way to change the order of the ILLUMINACLIP in Galaxy? In galaxy it is always performed initially. Ex: I need to perform CROP action first, then comes the ILLUMINACLIP. Thanks in advance. Regards, Dineli ...
illuminaclip trimmomatic options tool-form order written 15 months ago by dineli_karunathilaka10 • updated 15 months ago by peter.briggs20
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Answer: A: Trimmomatic tool is not visible in the workflow editor
... Hi Jen, Thanks for the reply. I'm using Galaxy 15.03 version. Do you think I need a upgrade? I installed trimmomatic using galaxy tool shed and tried manual installation as well. But same issue. And i did restart the server. I have installed galaxy using https://bitbucket.org/apetkau/galaxy-dis ...
written 16 months ago by dineli_karunathilaka10
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Trimmomatic tool is not visible in the workflow editor
... Hi, I have a local galaxy instance and have installed many tools from the galaxy tool shed. Recently I have installed Trimmomatic tool and installation was successful but when I go to build a workflow, trimmomatic tool is not visible in the tool panel. It works fine in all other places. Can some on ...
trimmomatic local tool workflow admin written 16 months ago by dineli_karunathilaka10

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